Gene patenting and free software: a breakthrough | Opensource.com

Last week, to the surprise of patent lawyers and the biotechnology industry, advocates for technological freedom won an enormous victory against socially harmful distortions of patent law. The Federal District Court for the Southern District of New York held invalid patents owned by Myriad Genetics on diagnostic testing for genetic susceptibility to the most common hereditary forms of breast and ovarian cancer. By "patenting" the right to determine whether the BRCA1 and BRCA2 genes are present in the relevant mutated form in a women's genome, Myriad Genetics has been able to exclude all other laboratories from conducting the test. Patients and their insurers have paid much more, and women and their families have waited crucial weeks longer than necessary for information relevant to treatment and potentially affecting survival.

The Public Patent Foundation and the American Civil Liberties Union challenged the patent on the ground that the Act does not permit the patenting of "facts of nature." In a lengthy and carefully argued opinion granting summary judgment, Judge Robert Sweet agreed. Judge Sweet rejected the basic premise on which gene testing patents such as the one granted to Myriad have been justified: that the amplification of naturally-occurring DNA sequences is a patentable transformation of the DNA molecule. Instead, Judge Sweet adopted the view put forward by Myriad's own expert witnesses, that DNA is a special molecule, "a physical carrier of information," and therefore held that the reading of such naturally-occurring information is not patentable subject matter. Whether posed as a new composition of matter, or as a method for "analyzing" or "comparing" DNA sequences, Judge Sweet held, Myriad's attempt to gain a monopoly on looking at a particular DNA sequence to find out what it says falls outside the permissible scope of patent law.

In reaching his legal conclusions, Judge Sweet relied significantly on the recent opinion of the Court of Appeals for the Federal Circuit, which has primary responsibility for interpreting the nation's patent law, In re Bilski, 535 F.3d 943 (2008), now pending in the Supreme Court. Bilski, as readers here will know, raises issues concerning the patentability of business methods and computer software, on essentially the same basic ground: that, as the Supreme Court has said, "phenomena of nature, though just discovered, mental processes, and abstract intellectual concepts are not patentable, as they are the basic tools of scientific and technological work." Gottschalk v. Benson, 409 U.S. 63, 67 (1972). Judge Sweet's opinion may be said to raise the stakes on Bilski slightly, but the parts of the Federal Circuit opinion on which Judge Sweet relies are not about the "specialized machine or transformation of matter" test adopted by the Federal Circuit to distinguish patentable from unpatentable inventions involving computer software and methods of doing business. Judge Sweet followed the Federal Circuit closely in its expression of the settled law of patent scope, making it more unlikely that the Federal Circuit, which will hear the inevitable appeal from Judge Sweet's judgment, will be inclined to disturb the conclusion.

Instead, Judge Sweet's ruling shows the beginning of a broader front in the judicial determination to reign in patenting that has gone too far, turning information that should be free to all into property exclusively held by a few. Neither our patent law itself, nor the guarantees of freedom to learn and teach protected by the First Amendment, can tolerate the widespread creation of statutory monopolies on ideas. Judge Sweet's conclusion with respect to gene patenting confirms and supports the position taken by the amici curiae in Bilski, including the Software Freedom Law Center, that computer software standing by itself, another carrier of information about algorithms, or mental processes, is not within the scope of patent law. Judge Sweet's opinion illuminates another of the large classes of human knowledge presently being made the subject of statutory monopolies through the patent system, but which cannot legally be made monopolies at all.

Americans have begun to understand a little bit about how, in the last two decades, corporations and their servants turned more and more of our society's opportunities into property for themselves. The sorrow and anger that is entering our politics, as honorable working people realize how badly they were had, will not soon abate. That the patent system too was gamed by the powerful at the expense of everybody else has not been fully grasped yet. But it will be. Time will show that Judge Sweet was more than courageous in his ruling, that he was also speaking with the voice of America behind him, as all great judges do.

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24 Comments

Thankyou Eben for your tireless work and this latest reporting. I am very grateful that the FLOSS community has you on its side. We would be lesser if it were not for your influence in all matters of IP law. Thankyou once more for passing this word.

"Judge Sweet's opinion may be said to raise the stakes on Bilski slightly"

I think that depends a lot on how broadly the Supreme Court rules in the Bilski case. If the Supreme Court rules that carriers of information about algorithms, or mental processes, is not within the scope of patent law then that ruling will sink gene patents before Myriad ever reaches the Supreme Court.

If the Supreme Court decides Bilski on very narrow grounds and does not rule on whether algorithms and mental processes are patentable then the Myriad case will give us another kick at the can when it reaches the Supreme Court. We could submit an amici curiae in the Myriad case which would ask for a broad enough ruling to abolish software patents as well as gene patents.

I especially appreciated the context that you put this into, the use of patents by the powerful to extract rents from society, and the slow but inevitable backlash this is causing. It's the failure of the state to protect the weak against the powerful that is the greatest injustice, and the one that motivated many of us to work against software patents (and more broadly, the patent system as a tool for large businesses to take ownership of our future).

Excellent post and a great victory for the open source community and the rest of the world. I had to laugh when I read the comment from brotherred about the FLOSS community I wasn't expecting anyone to go all dental about this. I am sure he meant FOSS.

Personally, I always use the term FLOSS because the word "free" in English can mean both "free as in beer" and "free as in liberty". French and Spanish don't have this problem: "free as in beer" is "gratuit" or "gratis", while "free as in liberty" is "libre". Including the "L" shows we mean liberty, not beer.

A patent grants the proprietor thereof a limited monopoly for a period of about 20 years. Eben speaks in his article of "... corporations and their servants turned more and more of our society's opportunities into property for themselves." What you need to remember is that these corporations spend millions and millions of dollars on research and development, without which, "society's" opportunities would not even have existed.

You fail to grasp that the limited monopoly is the pay-off for the millions and millions of dollars spent on research and development. If there is no pay-off, no monopoly to be gained, for making scientific breakthroughs, the "corporation scum" will not be investing in research and development and society's opportunities will disappear.

Maybe you see this as a battle won for the people, but I tell you, you celebrate future generations being deprived of some possibly awesome scientific breakthroughs.

What is the payoff from images from the Hubble Telescope? What is the payoff from the data gathered from the Mars rovers? What is the payoff from data gathered from *any* basic research function?

The flaw in your analysis is that every scientific endeavor *must* have an economic payoff in order to advance. There are many scientific challenges that have no known short-term economic benefit, yet are funded. Ever heard of the Large Hadron Collider? What do you expect to patent from the discovery of the hadron subatomic particle?

Images and data collected by these projects are not patentable, you cannot protect images and data. The true value lies in the inventions derived from this research and I submit again, that if there isn't at least a probability for economic payoff, research projects, such as those you have mentioned above, will not be undertaken and the images from the hubble telescope, and the data from the Rovers, will never have been taken or gathered.

I agree that it is possible that there may be some research purely devoted to understanding and broadening knowledge, but who will fund this? At the end of the day we need these corporations to fund these awesome projecst so that society's knowledge base is broadened. And giving them the fruits of their discoveries (for a limited period of 20 years) seems like a small price to pay.

@patentprofessional "I agree that it is possible that there may be some research purely devoted to understanding and broadening knowledge, but who will fund this?"

EPA, DOE,NIH, USGS, NOAA, NASA, DOD... Just a few.

"At the end of the day we need these corporations to fund these awesome projecst so that society's knowledge base is broadened."

What corporate fundamental research can you cite? I've just listed seven agencies that fund *basic* research - research that has no certainty of generating any income but attempts to answer a question of a fundamental scientific nature (i.e., what happens to subatomic particles at higher energies than 14 MeV?). I doubt that you can name one other than IBM now that Bell Lab's is essentially dead.

The idea of a monopoly as a reward is misplaced. The criteria that progress needs to be promoted was a great way to perhaps allow for monopolies as a possibility but has been ignored. If when the nation was just starting off with much wilderness around us, one patent examiner, much to be copied from European inventions not patented here, and very high costs and risks to many types of activities, we have clearly come a long long way since then to still be enabling these long monopolies, especially in fields with many participants and low costs (not to mention that copyright applies). There are better ways to reward innovation, assuming it isn't rewarded by the market itself.

And if FOSS has shown one thing it is the value of collaboration (vs. monopolizing) and that money is clearly not "everything" or even the main motivator in many cases.

To patentprofessional:
I am a scientist. You are talking about science done by corporations. Are you saying they are the authors of all discoveries in science, and therefore, they deserve to be paid for? My answer is, most science, the true discoveries, have been done by scientists from universities and institutions using the public's money (taxes). Corporations are money makers. That is their true color: they just want to squize money from anyone. How they do it? They look into the literature, the PUBLIC scientific literature available to everyone, and mostly published by laboratoires from universities and institutes around the globe. Then use this information in their profit. A company then produces a drug and sell it to the public at very high price. That is in short. But tcompanies are far from being honest though. How many drugs have been removed from the market because they are dangerous? So, don't assume these companies are victims of a complot.

I understand your point, and I assume from your post that you gain satisfaction from your research merely by broadening society's knowledge base. I respect that, I really do, but as you stated above, you are paid with public funds. Those funds come from corporations and institutions who, as you mentioned, are the money makers. Were it not for the corporations, your publicly funded research would never have existed and future generations will be deprived of your research.

I am not saying that only corporations deserved to be paid for their breakthroughs. Unfortunately, they are the only ones who use the patent system the way it should be used. They protect their inventions so that they can make more profit, and in return, their inventions fall into the public domain after 20 years.

>> Those funds come from corporations and institutions who, as you mentioned, are the money makers.

The funds come from everyone. The corporations are already getting a huge raw deal with this thing called limited liability.

The patent system is not really exploitable by the majority of us for gain (too expensive to acquire, maintain, and litigate), so it should not be usable against the majority of us.

Weren't patents supposed to be to prevent the giant imitators from copying the poor little inventor? Well? Why don't we encode that into the law? Fair use for patents should be automatic for every small firm. Patents are very broad, easy to copy off others who can't afford them and work publicly, expensive to defend against even when you know of prior art, not respectful of independent invention, have a ridiculously low bar for inventiveness (see "bell curve"), (for software) stifle a great very many, etc, etc, etc.

There is so much wrong with the notion of patent as necessary (and sole) means to incentivize R&D that I think the best response is a reference to a textbook.

The granting of patents in some area is, of course, only justifiable at all if it is significantly beneficial to scientific and technological progress and social welfare. That is something to bear in mind in view of the fact that 'gene patents' apparently haven't done much harm to research - yet!

I do not think that a patent is the sole means of incentivizing R&D. Quite frankly there are many ways to incentivize R&D, for example, war or disaster. However, in the absence of war or disaster, monetary gain is a driving force that pushes the boundaries of technology.

If this monetary gain drives technology forward, how can you say that it is not beneficial to scientific and technological progress?

We are talking about the effects of patents - not “monetary gain” - on progress and welfare. You obviously haven't read that book I linked to (it's free to download, btw) or any other on innovation economics. Not only can patents fail to be beneficial (even just to the sci. and tech. progress part of the equation), there are several well-known instances in history where they clearly have retarded progress. For a salient and recent example of one way this can happen see e.g. An Empirical Look At Software Patents by Bessen and Hunt.

@patentprofessional "However, in the absence of war or disaster, monetary gain is a driving force that pushes the boundaries of technology."

What economic benefit was bestowed on the early researchers in electromagntics? How much money did Faraday make for his discoveries? How much did Leo Szilard make for his discoveries? What was Einstein's net worth at the time of his death due to the publication of his papers in 1905 and 1917? How much money did Feynman get for his discoveries? Other than the Nobels that many of these researchers received, they saw nothing in real economic terms from their works - except for the recognition of their contribution.

Don't you concede that people are motivated by things other than money?

We can simply ask this, is writing quality software or doing quality science something that would not be done unless a broad patent monopoly were to be awarded?

Of course these activities don't need patents for "motivation". History and a simple survey makes it very clear that writing good software is within the reach of many people, especially when they collaborate, since no huge monetary investment needed and the knowledge is readily accessible as well. Further, success comes with many benefits, so, from professionals to hobbyists, achieving quality software can be extremely rewarding.

Seen a little differently, a patent monopoly is extremely toxic and stifling. It is a very unjust abridgment on the rights of millions and on our ability to pursue great advancement and satisfaction.

I had to go read the article again because I had almost forgotten about this thread.

Let me start off by saying that I work with patents every day. I am also 'n great supporter of open source software and on a very fundamental level, I agree with the basic principles of communism as laid down by Marx.

That being said, you can understand that I have debated the topic of patents frequently and have often struggled with the ethics of patents per se.

You have to understand that you can't just get a patent for anything. An invention has to be both new and inventive before it will be granted. The words "new" and "inventive" may seem simple, but they are actually quite stringent. To be new, an invention must not have been known, anywhere in the world before the date of filing of the patent application. To be inventive the invention must involve an inventive step and this step must not have been obvious to a person skilled in the relevant field, considering everything available to the public at the date of filing.

My personal view is that if these two (very stringent) requirements are satisfied, a person should be entitled to a patent. Historically, patents were introduced to prevent so called "black boxing", particularly in the agricultural industry where a new invention may increase yield, profitability or some other attribute of the industry. The idea was that it is better for such inventions to become part of public knowledge than be hidden away and only used by the inventor thereof. A patent specification must include an adequate description of an example of the invention to enable a person skilled in the field to exercise the invention. The quid pro quo is that your new, inventive invention becomes part of the public knowledge in exchange for a state granted monopoly of 20 years.

Now I realise that 20 years is a very long time in the software industry, but I would rather suggest attacking the period of the monopoly than being inherently biased against patents. As a mental exercise try to imagine what the software industry would be like if the development of early UNIX and DOS systems weren't blackboxed as they were and if they were only protected by patents in respect of new and inventive inventions. Licence fees would be paid for the new and inventive parts only for 20 years, thereafter it is public knowledge. There would have been less replication of code and the innovations that were made would have been properly rewarded. Perhaps I am biased because I work in this field but I truly believe that patents aren't inherently evil and fundamentally they reward innovation.

There are also mechanisms built into most patent systems to prevent abuse. In this regard I suggest that those of you who aren't familiar with the concept read up on compulsory licences and revocation of patents.

I believe the greatest obstacle in using the patent systems as it is meant to be used is cost. It is extremely expensive, if not nearly impossible for an individual to enforce his rights or defend himself against patent infringement proceedings. But this is of course a problem with th legal system itself and not just patent law. I would be all for any alternative that would decrease costs of patent suits and expedite such proceedings.

Maybe someone can invent such an alternative, and file a patent for it ;), at least then in 20 years the system might be more effective.

I agree with you that the costs of the system make patents that much more unbearable and unfair to most individuals and small businesses.

Of course, patents were not placed into law to apply to mere information (which is what software is.. information fed to a general purpose machine that will afterward behave as predicated) and were generally intended to serve as an incentive to raise large capital required to implement and distribute the invention and not get done in by larger competitors.

>> The words "new" and "inventive" may seem simple, but they are actually quite stringent. To be new, an invention must not have been known, anywhere in the world before the date of filing of the patent application.

Patent examiners don't look everywhere in the world (or US) as you almost seem to imply. In fact, I suspect there isn't a single patent examiner in the USPTO today that has analyzed or even skimmed 1/1000ths of 1% of the public source code that has been written in the prior 2 decades. That's an awful lot of material they don't know about when they grant a patent.

Truly, no one knows who is the first.

But if we did, this would hardly be a reason to consider taking away from society the natural ability of citizens and inventors to freely recreate those things for themselves.

Consider that software creations are information and expression. We not only have a First Amendment violation but software is within the purvue of ordinary folks so that 20 year monopolies are a sure way to stifle development and progress.

Einstein need sophisticated help an access to many advanced things and contemporary developments from peers in order to have been able to place himself into a position to have made his discoveries. If that information had been patented (or patentable), we would have suffered much.. and not just for Einstein's contributions but generally for those of many many others.

Same applies in music and many other areas where access to development is cheap, so there is much strength and progress made by society from collaboration and plentiful access.

>> To be inventive the invention must involve an inventive step and this step must not have been obvious to a person skilled in the relevant field, considering everything available to the public at the date of filing.

Red Hat spent $3 million to show that a few patents being used against them recently had significant prior art. The patents were nullified but at great cost to them and to those who use their software.

But we already know the USPTO doesn't really know what is new. Without knowing this, they can't make a good judgment call either on inventiveness. Though if they could, the ridiculously low standard would still lead to horribly stifling monopolies.

Let me ask you something. Do you make reference to the inventiveness bar ("non-obvious to a PHOSITA") with a straight face?

Do you know how many things are not obvious to a PHOSITA yet a PHOSITA discovers without help within one single year? Do you know how many things are not obvious to a PHOSITA but ridiculously obvious to many above average and genius software developers? Do you know how many above average and genius software developers practice the art today? [Take a hint from the bell curve, applied to the millions practicing sw dev today] That is an awful lot of smart brains to handcuff.

In fact, while those who find many things easy are developing more complex ideas that go beyond the "non-obvious to a PHOSITA", some PHOSITA who find many things non-obvious and have money are patenting away the basic building blocks of the really advanced stuff.

And let's not forget that it's rather easy to see what open source competitors are doing and then patent a little ahead of them to unfairly block their progress (or at least be able to present a claim) and hurt society.

>> The idea was that it is better for such inventions to become part of public knowledge than be hidden away and only used by the inventor thereof.

The tragic comedy is that by still allowing trade secrets on top of patenting, now the public gets the worst of both worlds. If an invention is a decent one, the firm keeps it as a trade secret. If the invention is something others will discover for themselves soon or perhaps already have, then filing a patent application first offers a way to put large wealth to work getting government hand-out (some would say communistic) 20-year monopolies.

And we know that the incentives go way down to work hard when you are given a guaranteed market where competitors are not allowed to compete.

>> As a mental exercise try to imagine what the software industry would be like if the development of early UNIX and DOS systems weren't blackboxed

BSD (a UNIX) has been around decades. Linux has been around now for almost exactly 2 full decades as well. Great visual and usable products have come and gone since computers have been affordable by individuals, and this has had nothing to do with "blackboxing". Their demise has to do with the natural propensity of software to become monopolies when the source code is not open and is actively developed by market leaders for incompatibility (it's natural to accidentally develop incompatibilities and deviations from specs, but surely the problem is made worse when this effort is made intentional to procure and defend a monopoly). In many cases, the network effects lock competitors out rather naturally and lock people in to single vendors. Black boxing has nothing to do with this, and we have seen much development in the past few decades.

>> Licence fees would be paid for the new and inventive parts only for 20 years, thereafter it is public knowledge.

Imagine if in practice we had to allow 20 year monopolies for all of the great software features of the last 10 years which overlapped with patented ideas that were ridiculously easy to rediscover (or were already known) and were derived by many firms surely at least because of how easy the concepts are to a team of engineers of diverse backgrounds working for a few years. If in practice we had to wait for 20 years for each such software feature, we'd be in bad shape today, especially since many things have leveraged other things which have leveraged other things etc.. all based on patented broad ideas (non-obvious to a PHOSITA).

Instead, we have gotten a lot of advancement (especially with serious doubt, both before and after Bilski, about the patentability of software); however, we also have been getting a lot of wasted money (many billions) in lawsuits and going to people who contributed next to nothing to this progress and development. We've also had wasted effort reinventing wheels merely "non-obvious to a PHOSITA" and have had to deal with chilling effects and unfair exits from the market.

Software is cheap to develop and distribute. It is information which benefits greatly form collaboration and is hurt by monopolies. It is not effectively a scarce product. Because of this and the ability for a nearly perfect tool (the computer) to help us "debug" it and reuse it almost in unlimited fashion, it can get very complex and is particularly threatened by idea monopolies when enforced.

Software is mathematics, yet has even already been ruled to be copyrightable (a normally much more narrow form of monopoly than patents).

>> There are also mechanisms built into most patent systems to prevent abuse.

Granting software patents (especially of such a low standard as non-obvious to a PHOSITA) and claiming the law and Constitution allows them is horrible abuse itself. The USPTO has already made their decision and failed society.

Most who can afford to take software patents to the SCOTUS have no interest in seeing a clear ruling against software patents. Most who don't want patents find it at some point much cheaper to settle, especially as the offer improves if it appears the patents might be invalidated.

Awesome ruling, well written article Eben! Very informative on first reading.

Would like to raise the question of how this might translate to plant genetic modifications? I see easy translations in the area of plant GMO's. These also have some connection to long term socially harmful results.

The more general fields of herbicides, insecticides and fungicides in agricultural and food production also would seem to have some connection. Our entire food production and delivery system in present time seems to be controlled or highly leveraged to a few similar type patents.

Who is sufficiently knowledgeable and resourceful enough to take up the challenge of harmful patents in our food system?

Thank you so much for writing this article and keeping everyone informed of the status of the 'Patent Wars'. There are a lot of people out there who have no idea what battles are being fought to protect their freedoms.

I think the work of the FSF, SFLC, Groklow and all the other OS organizations are extremely important in deciding what future direction our world is going to take. If it wasn't for the people tirelessly fighting IP/patent laws, we would be heading for a very dark future indeeed(think mega-corporations[eg. Blade Runner] ).

I have some friends (a labtech and a ct tech) who might be interested in this article. I hope to convince them to send this to their coworkers. Thanks again.

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